US6998484B2 - Synthesis of purine locked nucleic acid analogues - Google Patents

Synthesis of purine locked nucleic acid analogues Download PDF

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US6998484B2
US6998484B2 US09/971,364 US97136401A US6998484B2 US 6998484 B2 US6998484 B2 US 6998484B2 US 97136401 A US97136401 A US 97136401A US 6998484 B2 US6998484 B2 US 6998484B2
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optionally substituted
alkyl
carbonyl
aryl
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Troels Koch
Flemming Ressig Jensen
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Roche Innovation Center Copenhagen AS
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Santaris Pharma AS
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom

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  • the present invention relates to a new strategy for the synthesis of purine LNA (Locked Nucleic Acid) analogues which provides higher overall yields, and thus more cost efficient than previously known methods for the synthesis of purine LNA analogues.
  • purine LNA Locked Nucleic Acid
  • the present invention provides a novel strategy for the synthesis of purine LNA analogues comprising a regioselective 9-N purine glycosylation reaction followed by a one-pot nucleophilic aromatic substitution reaction of the 6-substituent in the purine ring and simultaneous nucleophile-induced intramolecular ring closure of the C-branched carbohydrate to form novel purine LNA analogues.
  • the novel strategy is demonstrated by the synthesis of the novel compound (1S,3R,4R,7S)-7-benzyloxy-1-methanesulfonylmethyl-3-(guanin-9-yl)-2,5-dioxabicyclo[2.2.1]heptane which is easily converted into (1S,3R,4R,7S)-7-hydroxy-1-hydroxymethyl-3-((2-N-isobutyrylguanin-9-yl)-2,5-dioxabicyclo[2.2.1]heptane after isobutyryl protection of the 2-amino purine group and subsequent substitution of 1-methanesulfonyl with benzoate, debenzoylation and debenzylation.
  • the novel strategy can easily be extended to the synthesis of purine LNAs containing other 6-substituted analogues and can be further extended to other heteroatoms than oxygen in the bicycle, such as nitrogen and sulphur.
  • the present invention relates to a method for the synthesis of novel purine LNA analogues of the general formula I wherein the two geminal substituents J 1 and J 2 when taken together represent oxo or thiono, and when taken separately one of them represents OR 9 , NR 10 R 11 , or SR 12 , and the other together with J 3 represents a double bond; when J 1 and J 2 represent oxo or thiono, J 3 represents hydrogen;
  • the present invention also relates to compounds of the general formula I as defined above.
  • the present invention furthermore relates to a method for the synthesis of the key intermediate of the general formula II, said method comprising the following step:
  • the present invention furthermore relates to novel compounds of the general formula II as defined above.
  • FIG. 1 illustrates an overall synthesis of G-LNA utilising the invention.
  • FIG. 2 illustrates the novel strategy according to the invention comprising: regioselective 9-N purine glycosylation reaction followed by a one-pot nucleophilic aromatic substitution reaction of the 6-chloro in the purine ring and nucleophile-induced intramolecular ring closure of the C-branched carbohydrate to form guanine-9-yl LNA.
  • the present invention relates to a method for the synthesis of purine LNA analogues of the general formula I as defined above:
  • the method of the invention comprises treatment of the key intermediate of the general formula II as defined above: with a nucleophilic reagent.
  • the nucleophilic reagent is selected from optionally substituted hydroxy(C 1-6 -alkane), optionally substituted phenol, optionally substituted hydroxy(C 1-6 -alkyl)benzene, NH 3 , optionally substituted amino(C 1-6 -alkane), optionally substituted aniline, optionally substituted amino(C 1-6 -alkyl)benzene, optionally substituted thio(C 1-6 -alkane), optionally substituted benzenethiol, optionally substituted thio(C 1-6 -alkyl)benzene, M-K—OH, M-K—NH 2 and M-K—SH (e.g.
  • M is a flurophor (such as flourescein, pyrene, anthracene, etc.), biotin, anthraqinonyl, etc. and K is —(CH 2 ) n — such as described below).
  • flurophor such as flourescein, pyrene, anthracene, etc.
  • K is —(CH 2 ) n — such as described below.
  • the molar ratio between compound II and the nucleophilic reagent is typically in the range of 1:2 to 1:10, preferably 1:2-1:8, more preferably 1:2-1:6.
  • nucleophilic reagents when used in excess can bring about an additional elimination reaction of the initially formed substitution product affording the 6-oxo-and 6-thio purine LNA analogues.
  • a feature of these nucleophilic reagents is that they comprise an acidic ⁇ -hydrogen which can participate in a ⁇ -elimination reaction such as 3-hydroxypropionitrile, 3-mercaptopropionitrile, 2-hydroxy-ethylbenzene, 2-hydroxy-1-nitroethane.
  • the treatment of compound II with the nucleophilic reagent is typically performed at ⁇ 30° C. to 100° C., such as ⁇ 20° C. to 60° C.
  • the treatment of compound II with the nucleophilic reagent may be carried out in the presence of a non-nucleophilic strong base, such as NaH, LiH, lithium diisopropylamide, and lithium tert-butoxide.
  • a non-nucleophilic strong base such as NaH, LiH, lithium diisopropylamide, and lithium tert-butoxide.
  • the presence of a non-nucleophilic strong base will generate the desired nucleophile.
  • the treatment is performed in the presence of NaH or LiH, preferably NaH.
  • the treatment of compound II with the nucleophilic reagent typically is carried out in the presence of a solvent, such as tetrahydrofuran, toluene, xylene, benzene, diethyl ether, acetonitril, triethylamine, N,N-dimethylformamide, dimethylsulfoxide, dichloromethane, and 1,2-dichloroethane, preferably tetrahydrofuran.
  • a solvent such as tetrahydrofuran, toluene, xylene, benzene, diethyl ether, acetonitril, triethylamine, N,N-dimethylformamide, dimethylsulfoxide, dichloromethane, and 1,2-dichloroethane, preferably tetrahydrofuran.
  • each of the substituents A 1 , A 2 , A 3 , A 4 and A 5 represent —O—.
  • R 13 preferably represents hydrogen or methyl, most preferably hydrogen.
  • W represents OH, SH or NH 2 , preferably NH 2 .
  • substituents J 1 and J 2 together represent oxo or thiono, preferably oxo, and J 3 represent hydrogen.
  • J 1 represents OR 9 , NR 10 R 11 , or SR 12
  • J 2 together with J 3 represents a double bond.
  • X is selected from chloro, fluoro, bromo, iodo, CN, methanesulfonyl, ⁇ -toluenesulfonyl, preferably chloro.
  • n is an integer from 1 to 3, such as 1, 2 or 3, preferably n is 1.
  • Each of the substituents R 1 , R 2 , R 3 , R 4 , R 9 , R 10 , R 11 , and R 12 are preferably independently selected from hydrogen, methyl, trifluoromethyl, ethyl, propyl, iso-propryl, butyl, t-butyl, pentyl, cyclopentyl, hexyl, cyclohexyl, phenyl, benzyl, phenylethyl, ortho-, meta-, and para-methylbenzyl, 2-chlorobenzyl, 4-phenylbenzyl, 2-cyanoethyl, and “active/functional” groups where M designates psoralens, ethidium bromide, acridine, anthraquinone, biotin, rhodamine or fluorescein and K designates polyethylene glycol, polymethylene, etc.
  • K designates a single bond so that the “active/functional” part of the group in question is attached directly to the purine ring.
  • each of the substituents R 5 and R 7 independently represent methanesulfonyl, trifluoromethanesulfonyl, ethanesulfonyl, 2,2,2-trifluoroethanesulfonyl, propanesulfonyl, iso-propanesulfonyl, butanesulfonyl, nonafluorobutanesulfonyl, pentanesulfonyl, cyclopentanesulfonyl, hexanesulfonyl, cyclohexanesulfonyl, ⁇ -toluenesulfonyl, 2-chloro- ⁇ -toluenesulfonyl, ortho-, meta-, para-toluenesulfonyl, benzenesulfonyl, ortho-, meta-, para-bromobenzenesulfonyl, ortho-, meta-, para-bromobenzenes
  • R 5 and R 7 represent methanesulfonyl, trifluoromethanesulfonyl, ethanesulfonyl, 2,2,2-trifluoroethanesulfonyl, butanesulfonyl, nonafluorobutanesulfonyl, ⁇ -toluenesulfonyl, para-toluenesulfonyl, benzenesulfonyl, para-bromobenzenesulfonyl, para-nitrobenzenesulfonyl, trimethylsilyl, tert-butyldimethylsilyl, tert-butyldiphenylsilyl, tert-butylmethoxyphenylsilyl and tert-butoxydiphenylsilyl, preferably methanesulfonyl, trifluoromethanesulfonyl, para-toluene
  • R 5 and R 7 are identical and are selected from methanesulfonyl, trifluoromethanesulfonyl, ethanesulfonyl, 2,2,2-trifluoroethanesulfonyl, butanesulfonyl, nonafluorobutanesulfonyl, ⁇ -toluenesulfonyl, para-toluenesulfonyl, benzenesulfonyl, para-bromobenzenesulfonyl, and para-nitrobenzene-sulfonyl, preferably methanesulfonyl, trifluoromethanesulfonyl, para-toluenesulfonyl and para-bromobenzenesulfonyl, more preferably methanesulfonyl, and para-toluenesulfonyl, even more preferably methanesulfonyl, and methan
  • R 6 comprises benzyl, ortho-, meta-, para-methylbenzyl, 2-chlorobenzyl, 4-phenylbenzyl, tetrahydropyran-2-yl, benzoyl, phenyl, trimethylsilyl, triethylsilyl, triisopropylsilyl, dimethylisopropylsilyl, diethylisopropylsilyl, dimethylthexyl, isopropylsilyl, tert-butyldimethylsilyl, tert-butyldiphenylsilyl, tribenzylsilyl, tri-para-xylylsilyl, triphenylsilyl, diphenylmethylsilyl, di-tert-butylmethylsilyl, tris(trimethylsilyl)silyl, tert-butylmethoxyphenylsilyl, tert-butoxydiphenylsilyl among which
  • R 5 and R 6 together represent di-tert-butylsilylene, 1,3-(1,1,3,3-tetraisopropyl)disiloxanylidene or 1,3-(1,1,3,3-tetra-tert-butoxy)disiloxanylidene.
  • R 8 is selected from hydrogen, optionally substituted alkylcarbonyl (e.g. acetyl and trifluoroacetyl), optionally substituted aryl-carbonyl (e.g. benzoyl and m-trifluoromethylbenzoyl), tert-butyldimethylsilyl, tert-butyldiphenylsilyl, and 9-fluorenylmethyloxycarbonyl, with the proviso that when A 4 represent —NR 13 —, then R 8 is selected from trifluoroacetyl and 9-fluorenylmethyloxy-carbonyl.
  • alkylcarbonyl e.g. acetyl and trifluoroacetyl
  • aryl-carbonyl e.g. benzoyl and m-trifluoromethylbenzoyl
  • tert-butyldimethylsilyl tert-butyldiphenylsilyl
  • R 8 is selected from acetyl, benzoyl and m-trifluoromethylbenzoyl, preferably acetyl.
  • R 6 represents benzyl
  • R 5 and R 7 both represent methanesulfonyl
  • R 8 represents acetyl
  • a 1 , A 2 , A 3 , A 4 and A 5 all represent oxygen, X is chloro, W is NH 2 , both of the substituents R 5 and R 7 are methanesulfonyl, R 6 represents benzyl, R 8 represent acetyl and n is 1.
  • the present invention also relates to the compound of the general formula I as defined above, with the proviso that R 1 is not hydrogen and R 2 is not isobutyryl or vice versa when A 1 , A 2 , A 3 and A 4 all represent oxygen, R 5 is methanesulfonyl, R 6 is benzyl and n is 1.
  • the present invention furthermore relates to a method for the synthesis of the key intermediate of the general formula II, said method comprising the following step:
  • the glycosylation reaction is performed according to the Vorbrüggen glycosylation method involving the reaction of the starting material III with silylated purine in the presence of a Lewis acid.
  • the glycosylation reaction is performed as a “one-pot” Vorbrüggen glycosylation reaction involving the coupling of the starting material III with the purine.
  • the reaction can be facilitated in the presence of a silylating agent, such as N,O-bis(trimethylsilyl)acetamide (BSA) and 1,1,1,3,3,3-hexamethyldisilazane (HMDS), and/or a Lewis acid such as tin(IV)chloride and trimethylsilyl trifluoromethansulfonate (TMS-triflate).
  • a silylating agent such as N,O-bis(trimethylsilyl)acetamide (BSA) and 1,1,1,3,3,3-hexamethyldisilazane (HMDS)
  • HMDS 1,1,1,3,3,3-hexamethyldisilazane
  • a Lewis acid such as tin(IV)chloride and trimethylsilyl trifluoromethansulfonate (
  • the silylating agent is N,O-bis(trimethylsilyl)acetamide and the Lewis acid is trimethylsilyl trifluoromethansulfonate.
  • R 8 is selected from acetyl, benzoyl and m-trifluoromethylbenzoyl, preferably acetyl
  • R 14 is selected from acetyloxy, methoxy, ethoxy, chloride, fluroride, bromide, iodide and SC 6 H 5 , preferably acetyloxy and methoxy, even more preferably acetyloxy.
  • a 1 , A 2 , A 3 , A 4 and A 5 all represent oxygen, R 6 represents benzyl, R 5 and R 7 both represent methanesulfonyl, R 8 represents acetyl, and R 14 represents acetyloxy.
  • the present invention furthermore relates to compounds of the general formula II as defined above.
  • C 1-12 -alkyl means a linear or branched hydrocarbon group having 1 to 12 carbon atoms, such as methyl, ethyl, propyl, iso-propyl, butyl, tert-butyl, iso-butyl, pentyl, hexyl, and dodecyl.
  • C 1-6 -alkyl means a linear, or branched hydrocarbon group having 1 to 6 carbon atoms, such as methyl, ethyl, propyl, iso-propyl, butyl, tert-butyl, iso-butyl, pentyl, hexyl, in particular methyl, ethyl, propyl, iso-propyl, tert-butyl, and iso-butyl.
  • C 2-12 -alkenyl covers linear or branched hydrocarbon groups having 2 to 12 carbon atoms and comprising one unsaturated bond.
  • alkenyl groups are vinyl, allyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, dodecaenyl.
  • C 1-12 -cycloalkyl means a cyclic hydrocarbon group having 1 to 12 carbon atoms, such as cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl.
  • C 1-6 -cycloalkyl means a cyclic hydrocarbon group having 1 to 6 carbon atoms, such as cyclopentyl and cyclohexyl.
  • C 2-12 -cycloalkenyl covers cyclic hydrocarbon groups having 2 to 12 carbon atoms and comprising one unsaturated bond.
  • C 2-12 -alkynyl means a linear or branched hydrocarbon group having 2 to 12 carbon atoms and comprising a triple bond. Examples hereof are ethynyl, propynyl, butynyl, octynyl, and dodecanyl.
  • the term “optionally substituted” means that the group in question may be substituted one or several times, preferably 1-3 times, with group(s) selected from hydroxyl, C 1-6 -alkoxy, carboxyl, C 1-6 -alkoxycarbonyl, C 1-6 -alkylcarbonyl, formyl, aryl, aryloxycarbonyl, arylcarbonyl, heteroaryl, amino, mono- and di(C 1-6 -alkyl)amino, carbamoyl, mono- and di(C 1-6 -alkyl)aminocarbonyl, amino-C 1-6 -alkyl-aminocarbonyl, mono- and di(C 1-6 -alkyl)amino-C 1-6 -alkyl-aminocarbonyl, C 1-6 -alkylcarbonylamino, cyano,
  • hydroxyl, C 1-6 -alkoxy, carboxyl, aryl, heteroaryl, amino, mono- and di(C 1-6 -alkyl)amino, and halogen where aryl and heteroaryl may be substituted 1-3 times with C 1-4 -alkyl, C 1-4 -alkoxy, nitro, cyano, amino or halogen.
  • Aryl and heteroaryl may be substituted as specifically describe below for “optionally substituted aryl and heteroaryl”.
  • aryl means a fully or partially aromatic carbocyclic ring or ring system, such as phenyl, naphthyl, 1,2,3,4-tetrahydronaphthyl, anthracyl, phenanthracyl, pyrenyl, benzopyrenyl, fluorenyl and xanthenyl, among which phenyl is a preferred example.
  • heteroaryl means a fully or partially aromatic carbocyclic ring or ring system where one or more of the carbon atoms have been replaced with heteroatoms, e.g. nitrogen ( ⁇ N— or —NH), sulphur, and/or oxygen atoms.
  • heteroaryl groups examples include oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, pyrrolyl, imidazolyl, pyrazolyl, pyridinyl, pyrazinyl, pyridazinyl, piperidinyl, coumaryl, furyl, quinolyl, benzothiazolyl, benzotriazolyl, benzodiazolyl, benzooxozolyl, phthalazinyl, phthalanyl, triazolyl, tetrazolyl, isoquinolyl, acridinyl, carbazolyl, dibenzazepinyl, indolyl, benzopyrazolyl, phenoxazonyl.
  • the term “optionally substituted” means that the group in question may be substituted one or several times, preferably 1-5 times, in particular 1-3 times with group(s) selected from hydroxyl (which when present in an enol system may be represented in the tautomeric keto form), C 1-6 -alkyl, C 1-6 -alkoxy, oxo (which may be represented in the tautomeric enol form), carboxyl, C 1-6 -alkoxycarbonyl, C 1-6 -alkylcarbonyl, formyl, aryl, aryloxy, aryloxycarbonyl, arylcarbonyl, heteroaryl, amino, mono- and di(C 1-6 -alkyl)amino; carbamoyl, mono- and di(C 1-6 -alkyl)aminocarbonyl, amino-C 1-6 -alkyl-aminocarbon
  • Preferred examples are hydroxyl, C 1-6 -alkyl, C 1-6 -alkoxy, carboxyl, C 1-6 -alkoxycarbonyl, C 1-6 -alkylcarbonyl, aryl, amino, mono- and di(C 1-6 -alkyl)amino, and halogen, wherein aryl may be substituted 1-3 times with C 1-4 -alkyl, C 1-4 -alkoxy, nitro, cyano, amino or halogen.
  • tri(alkyl/aryl)silyl means a silyl group substituted with 0-3 alkyl groups and/or 0-3 aryl groups, with the provision that the total number of alkyl and aryl groups is 3, selected from trimethylsilyl, dimethylphenylsilyl, diphenylmethylsilyl, isopropyldimethylsilyl, tert-butyldimethylsilyl, tert-butyldiphenylsilyl, triethylsilyl, triisopropylsilyl, diethylisopropylsilyl, dimethylthexylisopropylsilyl, tri-para-xylylsilyl, triphenylsilyl, diphenylmethylsilyl, di-tert-butylmethylsilyl, tris(trimethyl-silyl)silyl, tert-butylmethoxyphenylsilyl.
  • dialkyldisiloxanylidene means siloxane substituted with 4 alkyl groups selected from 1,3-(1,1,3,3-tetraisopropyl)disiloxanylidene and 1,3-(1,1,3,3-tetra-tert-butoxy)disiloxanylidene.
  • Halogen includes fluoro, chloro, bromo, and iodo.
  • DNA intercalator means a group which can intercalate into a DNA or RNA helix, duplex or triplex.
  • functional parts of DNA intercalators are acridines, anthracene, quinones such as anthraquinone, indole, quinoline, isoquinoline, dihydroquinones, anthracyclines, tetracyclines, methylene blue, anthracyclinone, psoralens, coumarins, ethidium-halides, dynemicin, metal complexes such as 1,10-phenanthroline-copper, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium-cobalt-enediynes such as calcheamicin, porphyrins, distamycin, netropcin, viologen, daunomycin.
  • acridines quinones such as anthraquinone,
  • photochemically active groups covers compounds which are able to undergo chemical reactions upon irradiation with light.
  • functional groups hereof are quinones, especially 6-methyl-1,4-naphtoquinone, anthraquinone, naphtoquinone, and 1,4-dimethyl-anthraquinone, diazirines, aromatic azides, benzophenones, psoralens, diazo compounds, and diazirino compounds.
  • thermochemically reactive group is defined as a functional group which is able to undergo thermochemically-induced covalent bond formation with other groups.
  • functional parts thermochemically reactive groups are carboxylic acids, carboxylic acid esters such as activated esters, carboxylic acid halides such as acid fluorides, acid chlorides, acid bromide, and acid iodides, carboxylic acid azides, carboxylic acid hydrazides, sulfonic acids, sulfonic acid esters, sulfonic acid halides, semicarbazides, thiosemicarbazides, aldehydes, ketones, primary alkohols, secondary alkohols, tertiary alkohols, phenols, alkyl halides, thiols, disulphides, primary amines, secondary amines, tertiary amines, hydrazines, epoxides, maleimides, and boronic
  • chelating group means a molecule that contains more than one binding site and frequently binds to another molecule, atom or ion through more than one binding site at the same time.
  • functional parts of chelating groups are iminodiacetic acid, nitrilotriacetic acid (NTA), ethylenediamine tetraacetic acid (EDTA), aminophosphonic acid, etc.
  • reporter group means a group which is detectable either by itself or as a part of an detection series.
  • functional parts of reporter groups are biotin, digoxigenin, fluorescent groups (groups which are able to absorb electromagnetic radiation, e.g.
  • dansyl (5-dimethylamino)-1-naphthalenesulfonyl
  • DOXYL N-oxyl-4,4-dimethyloxazolidine
  • PROXYL N-oxyl-2,2,5,5-tetramethylpyrrolidine
  • TEMPO N-oxyl-2,2,6,6-tetramethylpiperidine
  • dinitrophenyl acridines, coumarins, Cy3 and Cy5 (trademarks for Biological Detection Systems, Inc.), erytrosine, coumaric acid, umbelliferone, texas red, rhodamine, tetramethyl rhodamine, Rox, 7-nitrobenzo-2-oxa-1-diazole (NBD), pyrene, fluorescein, Europium, Ruthenium,
  • paramagnetic probes e.g. Cu 2+ , Mg 2+
  • enzymes such as peroxidases, alkaline phosphatases, ⁇ -galactosidases, and glucose oxidases
  • antigens antibodies
  • haptens groups which are able to combine with an antibody, but which cannot initiate an immune response by itself, such as peptides and steroid hormones
  • carrier systems for cell membrane penetration such as: fatty acid residues, steroid moieties (cholesteryl), vitamin A, vitamin D, vitamin E, folic acid peptides for specific receptors, groups for mediating endocytose, epidermal growth factor (EGF), bradykinin, and platelet derived growth factor (PDGF).
  • biotin fluorescein, Texas Red, rhodamine, dinitrophenyl, digoxigen
  • Ligands can comprise functional groups such as: aromatic groups (such as benzene, pyridine, naphtalene, anthracene, and phenanthrene), heteroaromatic groups (such as thiophene, furan, tetrahydrofuran, pyridine, dioxane, and pyrimidine), carboxylic acids, carboxylic acid esters, carboxylic acid halides, carboxylic acid azides, carboxylic acid hydrazides, sulfonic acids, sulfonic acid esters, sulfonic acid halides, semicarbazides, thiosemicarbazides, aldehydes, ketones, primary alcohols, secondary alcohols, tertiary alcohols, phenols, alkyl halides, thiols, disulphides, primary amines, secondary amines, tertiary amines, hydrazines, epoxide
  • aromatic groups such as benzene, pyridine
  • spacer means a thermochemically and photochemically non-active distance-making group and is used to join two or more different moieties of the types defined above. Spacers are selected on the basis of a variety of characteristics including their hydrophobicity, hydrophilicity, molecular flexibility and length (e.g. see Hermanson et. al., “Immobilised Affinity Ligand Techniques”, Academic Press, San Diego, Calif. (1992), p. 137-ff). Generally, the length of the spacers is less than or about 400 ⁇ , in some applications preferably less than 100 ⁇ .
  • the spacer thus, comprises a chain of carbon atoms optionally interrupted or terminated with one or more heteroatoms, such as oxygen atoms, nitrogen atoms, and/or sulphur atoms.
  • the spacer K may comprise one or more amide, ester, amino, ether, and/or thioether functionalities, and optionally aromatic or mono/polyunsaturated hydrocarbons, polyoxyethylene such as polyethylene glycol, oligo/polyamides such as poly- ⁇ -alanine, polyglycine, polylysine, and peptides in general, oligosaccharides, oligo/polyphosphates.
  • the spacer may consist of combined units thereof.
  • the spacer includes a chemically cleavable group.
  • chemically cleavable groups include disulphide groups cleavable under reductive conditions, peptide fragments cleavable by peptidases, or selenides cleavable under oxidative conditions, etc.
  • nucleoside means a glycoside of a heterocyclic base.
  • nucleoside is used broadly as to include non-naturally occurring nucleosides, naturally occurring nucleosides as well as other nucleoside analogues.
  • Illustrative examples of nucleosides are ribonucleosides comprising a ribose moiety as well as deoxyribonuclesides comprising a deoxyribose moiety.
  • bases of such nucleosides it should be understood that this may be any of the naturally occurring bases, e.g. adenine, guanine, cytosine, thymine, and uracil, as well as any modified variants thereof or any possible unnatural bases.
  • 1,2-O-isopropylidene-3-O-benzyl-4-C-methanesulfonyloxymethyl-5-O-methanesulfonyloxymethyl- ⁇ -D-ribofuranose (2, 20 g, 43 mmol) is dissolved in acetic acid (175 ml), acetic anhydride (28 ml) is added and finally 320 ⁇ l concentrated sulphuric acid. The solution is stirred over night. The solution is then evaporated to half volume at a water bath temperature at 35° C. Then water (300 ml) is added. The formed emulsion is extracted 3 times with ether (150 ml) and twice with DCM (at this point an emulsion is formed).
  • the combined organic phases are washed twice with water and saturated HCO 3 ⁇ (intense CO 2 evolution).
  • the organic phase is evaporated to a syrup, redissolved in DCM (200 ml) and residual acetic anhydride is quenched by vigorously agitation in a two phase system of DCM and saturated HCO 3 ⁇ (150 ml). Additional HCO 3 ⁇ (solid) may be added if the aqueous phase turns acidic.
  • the organic phases are collected, dried (MgSO 4 ) and the DCM is evaporated to yield a thick syrup.
  • the ⁇ / ⁇ ratio can be seen from HPLC but there is no really difference in Rf (MeOH/DCM: 5:95) compared to the starting material.
  • the TLC is developed in 20% Sulphuric acid+heat.
  • This product is used without further purification.
  • N,O-bis(trimethylsilyl)acetamide (29.6 g, 35 ml) was added to a stirred slurry of (3) (30 g, 58.8 mmol) and 2-amino-6-chloropurine (12 g, 70 mmol) in 1,2-dichloroethane (dried over sieves, 450 ml) and the mixture was refluxed for 40 min. to give a homogenous solution. The mixture was then removed from the heat and trimethylsilyltriflat (22 ml, 118 mmol) was added dropwise. The reaction mixture was refluxed for another 2 h.
  • the reaction mixture was cooled to room temperature and a saturated aqueous solution of bicarbonate (400 ml) was added. The slurry was allowed to stir for 15 min, pH was adjusted to 7-8 using glacial acetic acid and the mixture was extracted with chloroform. The aqueous phase was extracted with AcOEt and chloroform and the organic phases were combined. The organic phase was washed with brine (2 ⁇ 250 ml) and bicarbonate (2 ⁇ 250 ml). The organic phase was dried over sodium sulfate and concentrated under reduced pressure to give compound (4) as a yellowish foam which expands during vacuum dessication
  • 1,2-O-Isopropylidene-3-O-benzyl-4-C-methanesulfonyloxymethyl-5-O-methanesulfonyloxymethyl- ⁇ -D-ribofuranose (23.0 g, 49.3 mmol) is suspended at 18° C. under an N 2 atmosphere in 82 ml acetic acid (99%) resulting in a light yellow suspension. After 10 minutes of stirring, the substance is still undissolved. Sulphuric acid (98%, 247 mg) dissolved in acetic acid (99%, 2 ml) is thereafter added to the reaction mixture.
  • the resulting blurred organic phase is transferred to a round-bottomed flask and is stirred with 25 ml fresh 1M K 2 SO 4 for 30 minutes after which the clear organic phase is separated in a separation funnel and dried over MgSO 4 (6 g).
  • the dried solution is filtrated on a G3 filter, which subsequently is washed with 50 ml methylene chloride.
  • the resulting light yellow solution is evaporated (Rotavapor, 53° C., 100 to 20 mbar).
  • the resulting pale yellow oil is dried intensively (1 mbar, 50° C.).
  • the yield is 27.6 g (102% including residual solvent), and is pure as determined by TLC (CH 2 Cl 2 /TBME/Et 3 N 9.5:0.5:0.1); Developer: MeOH/sulphuric acid 1:1.
  • 1,2-O-acetyl-3-O-benzyl-4-C(methanesulfonyloxymethyl)-5-O-methanesulfonyl oxymethyl-)- ⁇ -D-ribofuranose (3) (25.7 g, 50.4 mmol) is dissolved by gently heating in 242 ml MeCN (HPLC-grade) and is transferred to a 1
  • TMS-OTf (18.2 ml) is added dropwise over 10 minutes via a syringe and under N 2 .
  • the resulting clear red-orange solution is refluxed for 90 minutes.
  • the reaction mixture is shaken with 100 ml water and 120 ml CH 2 Cl 2 . The phases tend to emulsify.
  • Phase-separation An upper clear yellow aqueous phase and a lower yellow organic phase.
  • the aqueous phase is extracted with 100 ml methylene chloride.
  • the combined organic phases are washed with 100 ml 1M K 2 HPO 4 .
  • the yellow emulsion is filtered on G3 filter and the filter cake (excess chloroguanine) is washed with 20 ml methylene chloride.
  • the aqueous phase is washed with 100 ml methylene chloride.
  • the organic phase is washed with 100 ml 1M K 2 HPO 4 ; phase separation.
  • 3-hydroxypropionitrile (14.84 g, freshly distilled) is dissolved in a 1
  • phase separation (aqueous phase lowest).
  • the aqueous phase is extracted with THF (50 ml).
  • the combined organic phases are extracted twice with NaCl (100 ml, 25%)+K 2 HPO 4 (25 ml, 1M). pH (resulting aqueous phase) 7.
  • the resulting organic phase (440 ml) is evaporated to near dryness. Re-dissolution in THF (250 ml) and evaporation again.
  • THF (50 ml) is added twice and evaporated to dryness. The remanence is suspended in 146 ml methylene chloride and the suspension is filtrated on G3. Wash with 53 ml methylene chloride.
  • the resulting solution is evaporated to dryness and the remanence is re-dissolved in 145 ml methylene chloride and transferred to a 3-necked flask with 5 ml CH 2 Cl 2 . 163 ml TBME is added dropwise and very slowly under vigorous stirring (300 rpm) to the red solution. After addition of 20 ml MTBE, yellow crystals precipitate on the side of the flask. The crystals are scraped into the solution with seed-crystals from the earlier batch. Over 90 minutes, 60 ml of MTBE is added and precipitation is initiated so that a blurred solution is formed. 80 ml added—clear precipitation of light crystals. The solution is seeded again.
  • Re-precipitation of the raw product 17.8 g of the filter cake is suspended in 50 ml DMSO in a flask equipped with a mechanical stirrer. The suspension is heated to 90° C. (contact thermometer) and 150 ml of ion exchanged water is slowly added dropwise with a stirring over 30 minutes at 85-90° C. After the addition of 30 ml, a precipitation of a substance on the side of the flask is observed, and after 60 ml precipitation occurs after each drop added. After the last addition, the heating cover is turned off and further 40 ml of water is added. The flask is stirred and allowed to cool to 20° C. Seeding at 50° C.
  • the flask is cooled in an ice-bath to 5° C. and the product is filtrated on a G3 filter. Wash with 2 portions of water (20 ml) and MTBE (30 ml) and dry in a hot-air cabinet. The yield is 15.0 g (66.7%) (94% pure by HPLC).
  • the pyridine residual can, if necessary, be removed by azeotropic distillation with toluene.

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US20020086998A1 (en) 2002-07-04
EP1334109B1 (de) 2006-05-10
JP2004510779A (ja) 2004-04-08
DE60119562T2 (de) 2007-05-10
DK1334109T3 (da) 2006-10-09
DE60119562D1 (de) 2006-06-14
JP4413493B2 (ja) 2010-02-10
ATE325806T1 (de) 2006-06-15
AU2001293687A1 (en) 2002-04-15
EP1334109A2 (de) 2003-08-13
WO2002028875A2 (en) 2002-04-11

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